That's my thoughts as well. Nobody cares about a stupid desert so they'd be the best ones to fill. The biggest thing would be to create inward flow from either pre-existing rivers or canal projects from elsewhere, and to prevent evaporation to allow water to collect and increase the size of lakes in those regions.
Chad basin is an endorheic basin, it's huge, but the lake inside is about 1/10th, 1/15th the surface area of the basin proper. Probably the best thing to do would be to cover the entire surface of the lake with shade balls, preferably just before a rainstorm, that way the lake will increase in size allowing any life living inside the water to be able to acquire sunlight in some areas where the sun will still be present, meanwhile the majority of the lake will be covered in anti-evaporation devices which will increase the size of the lake until the next rainstorm, at which point more shade balls will be added just beforehand to further increase the size of the lake gradually.
As for cryptorheic basins such as San Joaquin, these basins have rivers constantly outflowing into the oceans, so it's as simple as damming it up and letting water collect.
As for basins where no substantial bodies of water are present, such as Fezzan Basin, I'm not certain. I imagine water would have to be diverted from elsewhere, but as to where such water would be acquired i have no idea. It's obviously higher in altitude than the mediterranean sea and chad basin. Some combination of damming to prevent rain from escaping certain areas alongside anti-evaporation measures would make it hold enough water to expand in certain areas making the entire basin more wet as a result, at which point it's only a matter of time before the lake grows to full size.